embnmer.c

Function embNmerNuc2int

Encodes a word of a nucleic sequence into a unsigned ajlong ajint number. For a 4-byte unsigned ajlong ajint this will work if the word size is less than 16, otherwise there aren't enough bits to hold the number.

Synopsis

Prototype

ajulong embNmerNuc2int (
      const char* seq,
      ajint wordsize,
      ajint offset,
      AjBool* otherflag
);

Input

seq:(Input)the sequence to use
wordsize:(Input)the size of word of sequence to convert to int
offset:(Input)the offset into the sequence of the start of the word

Output

otherflag:(Output)set true if the sequence contains anything except A,G,C or T

Returns

ajulong:the encoded word

Description

Encodes a word of a nucleic sequence into a unsigned ajlong ajint number. For a 4-byte unsigned ajlong ajint this will work if the word size is less than 16, otherwise there aren't enough bits to hold the number.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embNmerInt2nuc

Decodes a unsigned long int number into a word of a nucleic sequence. The returned nucleic sequence is pre-pended to anything already in the string 'seq'.

Synopsis

Prototype

ajint embNmerInt2nuc (
      AjPStr* seq,
      ajint wordsize,
      ajulong value
);

Input

wordsize:(Input)the size of word to produce
value:(Input)the number to decode

Output

seq:(Output)the returned sequence

Returns

ajint:not used

Description

Decodes a unsigned long int number into a word of a nucleic sequence. The returned nucleic sequence is pre-pended to anything already in the string 'seq'.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embNmerProt2int

Encodes a word of a protein sequence into a unsigned ajlong ajint number. For a 4-byte unsigned ajlong ajint this will work if the word size is less than 8, otherwise there aren't enough bits to hold the number.

Synopsis

Prototype

ajulong embNmerProt2int (
      const char* seq,
      ajint wordsize,
      ajint offset,
      AjBool* otherflag,
      AjBool ignorebz
);

Input

seq:(Input)the sequence to use
wordsize:(Input)the size of word of sequence to convert to int
offset:(Input)the offset into the sequence of the start of the word
ignorebz:(Input)true if B and Z are to be treated as non-valid residues

Output

otherflag:(Output)set true if the sequence contains anything other than valid amino acid codes

Returns

ajulong:the encoded word

Description

Encodes a word of a protein sequence into a unsigned ajlong ajint number. For a 4-byte unsigned ajlong ajint this will work if the word size is less than 8, otherwise there aren't enough bits to hold the number.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embNmerInt2prot

Decodes a unsigned long int number into a word of a protein sequence. The returned protein sequence is pre-pended to anything already in the string 'seq'.

Synopsis

Prototype

ajint embNmerInt2prot (
      AjPStr* seq,
      ajint wordsize,
      ajulong value,
      AjBool ignorebz
);

Input

wordsize:(Input)the size of word to produce
value:(Input)the number to decode
ignorebz:(Input)true if B and Z are to be treated as non-valid residues

Output

seq:(Output)the returned sequence

Returns

ajint:not used

Description

Decodes a unsigned long int number into a word of a protein sequence. The returned protein sequence is pre-pended to anything already in the string 'seq'.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embNmerGetNoElements

Calculates the maximum number required to encode a sequence of size 'word'.

Synopsis

Prototype

AjBool embNmerGetNoElements (
      ajulong* no_elements,
      ajint word,
      AjBool seqisnuc,
      AjBool ignorebz
);

Input

word:(Input)the size of word to produce
seqisnuc:(Input)True is the sequence is nucleic, False if protein
ignorebz:(Input)true if B and Z are to be treated as non-valid residues

Output

no_elements:(Output)the returned number

Returns

AjBool:True if the word is small enough to be encoded in an ajulong

Description

Calculates the maximum number required to encode a sequence of size 'word'.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0